GapMind for catabolism of small carbon sources


Potential Gaps in catabolism of small carbon sources in Pseudomonas fluorescens FW300-N1B4

Found 38 low-confidence and 17 medium-confidence steps on the best paths for 62 pathways.

Pathway Step Best candidate 2nd candidate
D-serine dsdA: D-serine ammonia-lyase Pf1N1B4_1692 Pf1N1B4_2280
deoxyinosine deoB: phosphopentomutase Pf1N1B4_1165
deoxyinosine deoC: deoxyribose-5-phosphate aldolase
deoxyinosine nupC: deoxyinosine:H+ symporter NupC
deoxyribonate deoxyribonate-dehyd: 2-deoxy-D-ribonate 3-dehydrogenase Pf1N1B4_5039 Pf1N1B4_4556
deoxyribonate deoxyribonate-transport: 2-deoxy-D-ribonate transporter Pf1N1B4_5692 Pf1N1B4_4622
deoxyribonate ketodeoxyribonate-cleavage: 2-deoxy-3-keto-D-ribonate cleavage enzyme Pf1N1B4_2430
deoxyribose deoC: deoxyribose-5-phosphate aldolase
deoxyribose deoP: deoxyribose transporter
fucose fucA: L-fuculose-phosphate aldolase FucA Pf1N1B4_5075
fucose fucI: L-fucose isomerase FucI
fucose fucK: L-fuculose kinase FucK
fucose fucU: L-fucose mutarotase FucU
fucose HSERO_RS05255: ABC transporter for L-fucose, permease component Pf1N1B4_6033 Pf1N1B4_4287
fucose HSERO_RS05260: ABC transporter for L-fucose, substrate-binding component
glucose-6-P uhpT: glucose-6-phosphate:phosphate antiporter Pf1N1B4_2220
glucuronate exuT: D-glucuronate:H+ symporter ExuT
lactose lacP: lactose permease LacP
lactose lacZ: lactase (homomeric)
maltose susB: alpha-glucosidase (maltase) Pf1N1B4_835 Pf1N1B4_4677
mannose manP: mannose PTS system, EII-CBA components Pf1N1B4_1144
NAG nagA: N-acetylglucosamine 6-phosphate deacetylase
NAG nagB: glucosamine 6-phosphate deaminase (isomerizing) Pf1N1B4_1947
NAG nagEcba: N-acetylglucosamine phosphotransferase system, EII-CBA components
phenylacetate paaA: phenylacetyl-CoA 1,2-epoxidase, subunit A
phenylacetate paaB: phenylacetyl-CoA 1,2-epoxidase, subunit B
phenylacetate paaC: phenylacetyl-CoA 1,2-epoxidase, subunit C
phenylacetate paaE: phenylacetyl-CoA 1,2-epoxidase, subunit E Pf1N1B4_925
phenylacetate paaF: 2,3-dehydroadipyl-CoA hydratase Pf1N1B4_4788 Pf1N1B4_4777
phenylacetate paaG: 1,2-epoxyphenylacetyl-CoA isomerase / 2-(oxepinyl)acetyl-CoA isomerase / didehydroadipyl-CoA isomerase Pf1N1B4_4788 Pf1N1B4_679
phenylacetate paaK: phenylacetate-CoA ligase Pf1N1B4_575 Pf1N1B4_572
phenylacetate paaZ1: oxepin-CoA hydrolase Pf1N1B4_4788 Pf1N1B4_679
phenylacetate paaZ2: 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde dehydrogenase
phenylacetate ppa: phenylacetate permease ppa Pf1N1B4_3673
propionate putP: propionate transporter; proline:Na+ symporter Pf1N1B4_1487
rhamnose LRA1: L-rhamnofuranose dehydrogenase Pf1N1B4_4527 Pf1N1B4_5039
rhamnose LRA2: L-rhamnono-gamma-lactonase
rhamnose LRA4: 2-keto-3-deoxy-L-rhamnonate aldolase Pf1N1B4_5694
rhamnose rhaT: L-rhamnose:H+ symporter RhaT
thymidine deoB: phosphopentomutase Pf1N1B4_1165
thymidine deoC: deoxyribose-5-phosphate aldolase
thymidine nupG: thymidine permease NupG/XapB Pf1N1B4_4098
tryptophan antA: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), large subunit AntA Pf1N1B4_5800
tryptophan antB: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), small subunit AntB Pf1N1B4_5799
tryptophan antC: anthranilate 1,2-dioxygenase (deaminating, decarboxylating), electron transfer component AntC Pf1N1B4_5798
tryptophan kyn: kynureninase
tryptophan kynA: tryptophan 2,3-dioxygenase
tryptophan kynB: kynurenine formamidase
xylitol PLT5: xylitol:H+ symporter PLT5
xylitol xdhA: xylitol dehydrogenase Pf1N1B4_512 Pf1N1B4_5039
xylose gtsA: xylose ABC transporter, periplasmic substrate-binding component GtsA Pf1N1B4_596
xylose gtsB: xylose ABC transporter, permease component 1 GtsB Pf1N1B4_595
xylose gtsC: xylose ABC transporter, permease component 2 GtsC Pf1N1B4_594
xylose gtsD: xylose ABC transporter, ATPase component GtsD Pf1N1B4_593 Pf1N1B4_4847
xylose xylA: xylose isomerase

Confidence: high confidence medium confidence low confidence

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.



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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory